Mercurial > repos > ktnyt > gembassy
comparison GEMBASSY-1.0.3/doc/text/gaaui.txt @ 0:8300eb051bea draft
Initial upload
author | ktnyt |
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date | Fri, 26 Jun 2015 05:19:29 -0400 |
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1 gaaui | |
2 Function | |
3 | |
4 Calculates various indece of amino acid usage | |
5 | |
6 Description | |
7 | |
8 gaaui calculates amino acid usage indices for proteins (excluding | |
9 formylmethionine). Calculated indices are as follows, | |
10 Laa: Length in amino acids | |
11 ndaa: Number of different amino acids | |
12 Haau: Entropy of amino acid usage | |
13 mmw: Mean molecular weight | |
14 gravy: Mean hydropathic indices of each amino acid | |
15 aroma: Relative frequency of aromatic amino acids | |
16 | |
17 G-language SOAP service is provided by the | |
18 Institute for Advanced Biosciences, Keio University. | |
19 The original web service is located at the following URL: | |
20 | |
21 http://www.g-language.org/wiki/soap | |
22 | |
23 WSDL(RPC/Encoded) file is located at: | |
24 | |
25 http://soap.g-language.org/g-language.wsdl | |
26 | |
27 Documentation on G-language Genome Analysis Environment methods are | |
28 provided at the Document Center | |
29 | |
30 http://ws.g-language.org/gdoc/ | |
31 | |
32 Usage | |
33 | |
34 Here is a sample session with gaaui | |
35 | |
36 % gaaui refseqn:NC_000913 | |
37 Calculates various indece of amino acid usage | |
38 AAINDEX entry output file [nc_000913.gaaui]: | |
39 | |
40 Go to the input files for this example | |
41 Go to the output files for this example | |
42 | |
43 Command line arguments | |
44 | |
45 Standard (Mandatory) qualifiers: | |
46 [-sequence] seqall Nucleotide sequence(s) filename and optional | |
47 format, or reference (input USA) | |
48 [-outfile] outfile [*.gaaui] AAINDEX entry output file | |
49 | |
50 Additional (Optional) qualifiers: (none) | |
51 Advanced (Unprompted) qualifiers: | |
52 -[no]accid boolean [Y] Include to use sequence accession ID as | |
53 query | |
54 | |
55 Associated qualifiers: | |
56 | |
57 "-sequence" associated qualifiers | |
58 -sbegin1 integer Start of each sequence to be used | |
59 -send1 integer End of each sequence to be used | |
60 -sreverse1 boolean Reverse (if DNA) | |
61 -sask1 boolean Ask for begin/end/reverse | |
62 -snucleotide1 boolean Sequence is nucleotide | |
63 -sprotein1 boolean Sequence is protein | |
64 -slower1 boolean Make lower case | |
65 -supper1 boolean Make upper case | |
66 -scircular1 boolean Sequence is circular | |
67 -sformat1 string Input sequence format | |
68 -iquery1 string Input query fields or ID list | |
69 -ioffset1 integer Input start position offset | |
70 -sdbname1 string Database name | |
71 -sid1 string Entryname | |
72 -ufo1 string UFO features | |
73 -fformat1 string Features format | |
74 -fopenfile1 string Features file name | |
75 | |
76 "-outfile" associated qualifiers | |
77 -odirectory2 string Output directory | |
78 | |
79 General qualifiers: | |
80 -auto boolean Turn off prompts | |
81 -stdout boolean Write first file to standard output | |
82 -filter boolean Read first file from standard input, write | |
83 first file to standard output | |
84 -options boolean Prompt for standard and additional values | |
85 -debug boolean Write debug output to program.dbg | |
86 -verbose boolean Report some/full command line options | |
87 -help boolean Report command line options and exit. More | |
88 information on associated and general | |
89 qualifiers can be found with -help -verbose | |
90 -warning boolean Report warnings | |
91 -error boolean Report errors | |
92 -fatal boolean Report fatal errors | |
93 -die boolean Report dying program messages | |
94 -version boolean Report version number and exit | |
95 | |
96 Input file format | |
97 | |
98 The database definitions for following commands are available at | |
99 http://soap.g-language.org/kbws/embossrc | |
100 | |
101 gaaui reads one or more nucleotide sequences. | |
102 | |
103 Output file format | |
104 | |
105 The output from gaaui is to a plain text file. | |
106 | |
107 File: nc_000913.gaaui | |
108 | |
109 Sequence: NC_000913 | |
110 Laa,ndaa,Haau,mmw,gravy,aroma,gene | |
111 20,8,2.4842,117.48,+0.0150,0.0000,thrL | |
112 819,20,4.0887,126.65,+0.0328,0.0659,thrA | |
113 309,20,4.1228,126.35,+0.0181,0.0712,thrB | |
114 427,20,4.0806,128.00,-0.1014,0.0843,thrC | |
115 97,18,3.9165,133.54,-1.0268,0.0928,yaaX | |
116 257,19,4.0733,132.55,-0.4117,0.1089,yaaA | |
117 475,20,4.0413,126.46,+0.6781,0.1242,yaaJ | |
118 316,20,4.0395,128.99,-0.2165,0.0728,talB | |
119 | |
120 [Part of this file has been deleted for brevity] | |
121 | |
122 169,20,4.0001,124.90,+0.0231,0.0710,yjjX | |
123 214,20,3.9937,129.77,-0.3813,0.0374,ytjC | |
124 288,20,4.1421,132.58,-0.3628,0.1111,rob | |
125 156,20,4.0627,126.72,-0.0442,0.0705,creA | |
126 228,20,4.0471,131.94,-0.1408,0.0789,creB | |
127 473,20,4.0254,128.01,+0.0023,0.0677,creC | |
128 449,20,4.0871,128.66,+0.2082,0.0980,creD | |
129 237,20,4.0729,132.54,-0.4970,0.0675,arcA | |
130 45,15,3.5800,123.27,+0.7533,0.0222,yjjY | |
131 227,20,4.0283,128.63,-0.0031,0.0573,yjtD | |
132 | |
133 | |
134 Data files | |
135 | |
136 None. | |
137 | |
138 Notes | |
139 | |
140 None. | |
141 | |
142 References | |
143 | |
144 Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and | |
145 aromaticity are the major trends of amino-acid usage in 999 Escherichia | |
146 coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a | |
147 | |
148 Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga | |
149 maritima J Mol Evol. 54(5):563-8. | |
150 | |
151 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and | |
152 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench | |
153 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306. | |
154 | |
155 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for | |
156 large-scale analysis of high-throughput omics data, J. Pest Sci., | |
157 31, 7. | |
158 | |
159 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome | |
160 Analysis Environment with REST and SOAP Web Service Interfaces, | |
161 Nucleic Acids Res., 38, W700-W705. | |
162 | |
163 Warnings | |
164 | |
165 None. | |
166 | |
167 Diagnostic Error Messages | |
168 | |
169 None. | |
170 | |
171 Exit status | |
172 | |
173 It always exits with a status of 0. | |
174 | |
175 Known bugs | |
176 | |
177 None. | |
178 | |
179 See also | |
180 | |
181 gaminoinfo Prints out basic amino acid sequence statistics | |
182 gbui Calculates base usage indeces for protein-codin sequences | |
183 gcodoncompiler Calculates various kinds of amino acid and codon usage data | |
184 | |
185 Author(s) | |
186 | |
187 Hidetoshi Itaya (celery@g-language.org) | |
188 Institute for Advanced Biosciences, Keio University | |
189 252-0882 Japan | |
190 | |
191 Kazuharu Arakawa (gaou@sfc.keio.ac.jp) | |
192 Institute for Advanced Biosciences, Keio University | |
193 252-0882 Japan | |
194 | |
195 History | |
196 | |
197 2012 - Written by Hidetoshi Itaya | |
198 2013 - Fixed by Hidetoshi Itaya | |
199 | |
200 Target users | |
201 | |
202 This program is intended to be used by everyone and everything, from | |
203 naive users to embedded scripts. | |
204 | |
205 Comments | |
206 | |
207 None. | |
208 |